RaceID progenitor

Parameter settings

Import Seurat

Split data bei treatment and tissue group

Get differently expressed genes between condition

Create SCseq Object

SCseq filter data

Filterdata can be run with LBatch and bmode to remove genes associated with batch effects. VarID workflow also allows regression of batch effect in pruneKnn with regNB. in that case the regNB parameter of the compNoise function needs to be TRUE as well. Additional variables can be regressed out using the regVar variable with a data.frame. The rownames correspond to cell id and columns to values e.g. cell cycle.

Filtered expression matrix

Create variables for regression

Prune KNN and compute cluster with transition probabilities

Compute noise from corrected variance

Update SCseq object

Save output

Dimensional reduction

Plot

Combine VarID results Seurat object

UMAP reduction plots

Cluster label frequency NaCl

Cluster label frequency CpG